There is considerable interest in the role of oxygen-derived oxidants (often termed generically reactive oxygen species), and the potential effect of exogenous antioxidants, in the pathogenesis of infectious disease. Most of the published research focuses on the inflammatory response and the concept that oxidants are pro-inflammatory and antioxidants are anti-inflammatory. The present review discusses the evidence that both oxidants and thiol antioxidants are important in the various processes of innate and adaptive immunity, focusing on the function of the immune system in the defense against pathogens, rather than its pathogenic role in inflammatory and autoimmune disease.

Inorganic complexes of iron and sulfur, that is, iron-sulfur [FeS] clusters, have played a fundamental role in life on Earth since the prebiotic period. These clusters were involved in elementary reactions leading to the emergence of life and, since then, gained function in processes, such as respiration, replication, transcription, and the immune response. We discuss how three [FeS] proteins involved in the innate immune response play a role in oncogene expression/function and oncometabolism. Our analysis highlights the importance of future research into understanding the [FeS] clusters' roles in cancer progression and proliferation. The outcomes of these studies will help identify new targets and develop new anticancer therapeutics.

Metabolomics, the global profiling of small molecules in the body, has emerged as a promising analytical approach for assessing molecular changes associated with ageing at the population level. Understanding root metabolic ageing pathways may have important implications for managing age-related disease risk. In this short review, relevant studies published in the last few years that have made valuable contributions to this field will be discussed. These include large-scale studies investigating metabolic changes with age, metabolomic clocks, and metabolic pathways associated with ageing phenotypes. Recent significant advances include the use of longitudinal study designs, populations spanning the whole life course, standardised analytical platforms of enhanced metabolome coverage and development of multivariate analyses. While many challenges remain, recent studies have demonstrated the considerable promise of this field.

Peroxiredoxins (Prx), thiol-dependent peroxidases, were first identified as H2O2 detoxifiers, and more recently as H2O2 sensors, intermediates in redox-signaling pathways, metabolism modulators, and chaperones. The multifaceted nature of Prx is not only dependent on their peroxidase activity but also strongly associated with specific protein-protein interactions that are being identified, and where the Prx oligomerization dynamics plays a role. Their oxidation by a peroxide substrate forms a sulfenic acid that opens a route to channel the redox signal to diverse protein targets. Recent research underscores the importance of different Prx isoforms in the cellular processes behind disease development with potential therapeutic applications.

Over the last several decades, there has been continued interest in developing novel therapeutic approaches targeting protein lysine methyltransferases (PKMTs). Along with PKMT inhibitors, targeted protein degradation (TPD) has emerged as a promising strategy to attenuate aberrant PKMT activity. Particularly, proteolysis targeting chimeras (PROTACs) effectively eliminate PKMTs of interest, suppressing all enzymatic and non-enzymatic functions. PROTACs and other TPD approaches add new depth to PKMT research and novel therapeutics discovery. This review focuses on recent advances in PKMT degrader and inhibitor development over the last several years.

Liquid-liquid phase separation (LLPS) and liquid-solid phase transitions (LSPT) play crucial roles in biological systems, including sorting biomolecules, facilitate the transport of substrates for assembly, and accelerate the formation of metabolic and signaling complexes. Efforts towards improved characterization and quantification of phase separated species remain of outstanding interest and priority. In this review, we cover recent advances and the strategies used with small molecule fluorescent probes for the study of phase separation.

Recognition of the prevalence of hydropersulfides (RSSH) and characterization of their enhanced two-electron reactivity relative to thiols have led to their implication in maintaining cellular redox homeostasis, in addition to other potential roles. Recent attention on the one-electron reactivity of RSSH has uncovered their potent radical-trapping antioxidant activity, which enables them to inhibit phospholipid peroxidation and associated cell death by ferroptosis. Herein, we briefly review key aspects of the reactivity and underlying physicochemical properties of RSSH. We emphasize their reactivity to radicals-particularly lipid peroxyl radicals that propagate the lipid peroxidation chain reaction-and the recent recognition that this results in ferroptosis suppression. We highlight open questions related to recent developments in this area and, given that all living organisms possess the ability to synthesize persulfides endogenously, suggest they may be primordial radical scavengers that occurred early in evolution and still play a role today.

Heightened concentrations of reactive metabolites, including reactive oxygen species (ROS), can damage all macromolecules leading to the erosion of cellular fidelity. In this regard, the control of ROS in the nuclues is essential for cellular homeostasis, and dysregulation of nuclear ROS has been attributed to multiple pathologies and the mechanism of action of certain chemotherapies. How nuclear ROS is generated, detoxified and sensed is poorly understood, and stems in part, from a historical lack of tools that allow for its precise generation and detection. Here, we summarize the latest advances in chemical biology inspired approaches that have been developed to study nuclear ROS and highlight how these tools have led to major breakthroughs in understanding its regulation. The continued development and application of chemical biology approaches to understand nuclear ROS promises to unlock fundamental insights into human physiology and disease.

Thrombosis is the leading cause of death in many diseased conditions. Oxidative stress is characteristic of these conditions. Yet, the mechanisms through which oxidants become prothrombotic are unclear. Recent evidence suggests protein cysteine and methionine oxidation as prothrombotic regulators. These oxidative post-translational modifications occur on proteins that participate in the thrombotic process, including Src family kinases, protein disulfide isomerase, β2 glycoprotein I, von Willebrand factor, and fibrinogen. New chemical tools to identify oxidized cysteine and methionine proteins in thrombosis and hemostasis, including carbon nucleophiles for cysteine sulfenylation and oxaziridines for methionine, are critical to understanding why clots occur during oxidative stress. These mechanisms will identify alternative or novel therapeutic approaches to treat thrombotic disorders in diseased conditions.

Microbes utilize numerous metal cofactor-containing proteins to recognize and respond to constantly fluctuating redox stresses in their environment. Gaining an understanding of how these metalloproteins sense redox events, and how they communicate such information downstream to DNA to modulate microbial metabolism, is a topic of great interest to both chemists and biologists. In this article, we review recently characterized examples of metalloprotein sensors, focusing on the coordination and oxidation state of the metals involved, how these metals are able to recognize redox stimuli, and how the signal is transmitted beyond the metal center. We discuss specific examples of iron, nickel, and manganese-based microbial sensors, and identify gaps in knowledge in the field of metalloprotein-based signal transduction pathways.

In the review, current status of sulfoxides on the pharmaceutical market is discussed. In the first part of the article, natural sulfoxides will be described with a special focus on sulforaphane and amanitin, a mushroom toxin which has been developed as payload in antibody drug conjugates in the possible cancer treatment. Controversies associated with the medical use of dimethylsulfoxide are briefly described in the next section. In the part devoted to PPIs, the benefits of using pure enantiomers (chiral switch) are discussed. An interesting approach, repositioning of drugs is exemplified by new possible applications of modafinil and sulindac. The review is concluded by presentation of cenicriviroc and adezmapimod, both with the status of promising drug candidates.

Activity-based protein profiling (ABPP) is a powerful chemical approach for probing protein function and enzymatic activity in complex biological systems. This strategy typically utilizes activity-based probes that are designed to bind a specific protein, amino acid residue, or protein family and form a covalent bond through a reactivity-based warhead. Subsequent analysis by mass spectrometry-based proteomic platforms that involve either click chemistry or affinity-based labeling to enrich for the tagged proteins enables identification of protein function and enzymatic activity. ABPP has facilitated elucidation of biological processes in bacteria, discovery of new antibiotics, and characterization of host-microbe interactions within physiological contexts. This review will focus on recent advances and applications of ABPP in bacteria and complex microbial communities.

Mass spectrometry imaging (MSI) is an emerging technology in cancer metabolomics. Desorption electrospray ionization (DESI) and matrix-assisted laser desorption ionization (MALDI) MSI are complementary techniques to identify hundreds of metabolites in space with close to single-cell resolution. This technology leap enables research focusing on tumor heterogeneity, cancer cell plasticity, and the communication signals between cancer and stromal cells in the tumor microenvironment (TME). Currently, unprecedented knowledge is generated using spatial metabolomics in fundamental cancer research. Yet, also translational applications are emerging, including the assessment of spatial drug distribution in organs and tumors. Moreover, clinical research investigates the use of spatial metabolomics as a rapid pathology tool during cancer surgeries. Here, we summarize MSI applications, the knowledge gained by this technology in space, future directions, and developments needed.

Elucidating protein-protein interaction (PPI) networks and their structural features within cells is central to understanding fundamental biology and associations of cell phenotypes with human pathologies. Owing to technological advancements during the last decade, cross-linking mass spectrometry (XL-MS) has become an enabling technology for delineating interaction landscapes of proteomes as they exist in living systems. XL-MS is unique due to its capability to simultaneously capture PPIs from native environments and uncover interaction contacts though identification of cross-linked peptides, thereby permitting the determination of both identity and connectivity of PPIs in cells. In combination with high resolution structural tools such as cryo-electron microscopy and AI-assisted prediction, XL-MS has contributed significantly to elucidating architectures of large protein assemblies. This review highlights the latest developments in XL-MS technologies and their applications in proteome-wide analysis to advance structural systems biology.

Bacteria comprise complex communities within our bodies and largely have beneficial roles, however a small percentage are pathogenic. While all pathogens are important to public health, immediate action is necessary to combat bacterial strains developing pan- and multi-resistance to antibiotics. As present therapeutics fail to tackle this problem, novel strategies are required to address this threat. Activity-based probes (ABPs) are one method to investigate proteins of interest in pathogens. These probes can serve multiple purposes to better our understanding of bacterial pathogenicity. Herein, we highlight recent studies that used ABPs to identify new drug targets or visualize antibiotic resistance- or bacterial virulence-associated proteins, and introduce strategies to determine the specificity of ABPs within a targeted enzyme class.

Protein-protein and protein-RNA interactions are essential for cell function and survival. These interactions facilitate the formation of ribonucleoprotein complexes and biomolecular condensates via phase separation. Such assembly is involved in transcription, splicing, translation and stress response. When dysregulated, proteins and RNA can undergo irreversible aggregation which can be cytotoxic and pathogenic. Despite technical advances in investigating biomolecular condensates, achieving the necessary spatiotemporal resolution to deduce the parameters that govern their assembly and behavior has been challenging. Many laboratories have applied advanced microscopy methods for imaging condensates. For example, single molecule imaging methods have enabled the detection of RNA-protein interaction, protein-protein interaction, protein conformational dynamics, and diffusional motion of molecules that report on the intrinsic molecular interactions underlying liquid-liquid phase separation. This review will outline advances in both microscopy and spectroscopy techniques which allow single molecule detection and imaging, and how these techniques can be used to probe unique aspects of biomolecular condensates.

The long luminescence lifetimes and sharp emission bands of luminescent lanthanide complexes have long been recognized as invaluable strengths for sensing and imaging in complex aqueous biological or environmental media. Herein we discuss the recent developments of these probes for sensing metal ions and, increasingly, anions. Underappreciated in the field, buffers and metal hydrolysis influence the response of many responsive lanthanide probes. The inherent complexities arising from these interactions are further discussed.

DnaK is a chaperone that aids in nascent protein folding and the maintenance of proteome stability across bacteria. Due to the importance of DnaK in cellular proteostasis, there have been efforts to generate molecules that modulate its function. In nature, both protein substrates and antimicrobial peptides interact with DnaK. However, many of these ligands interact with other cellular machinery as well. Recent work has sought to modify these peptide scaffolds to create DnaK-selective and species-specific probes. Others have reported protein domain mimics of interaction partners to disrupt cellular DnaK function and high-throughput screening approaches to discover clinically-relevant peptidomimetics that inhibit DnaK. The described work provides a foundation for the design of new assays and molecules to regulate DnaK activity.

Chemical elements, especially metals, play very specific roles in the life sciences. The implementation of correlative imaging methods, of elements on the one hand and of molecules or biological structures on the other hand, is the subject of recent developments. The most commonly used spectro-imaging techniques for metals are synchrotron-induced X-ray fluorescence, mass spectrometry and fluorescence imaging of metal molecular sensors. These imaging methods can be correlated with a wide variety of other analytical techniques used for structural imaging (e.g., electron microscopy), small molecule imaging (e.g., molecular mass spectrometry) or protein imaging (e.g., fluorescence microscopy). The resulting correlative imaging is developed at different scales, from biological tissue to the subcellular level. The fields of application are varied, with some major research topics, the role of metals in the aetiology of neurodegenerative diseases and the use of metals for medical imaging or cancer treatment.

The objective of this review is to provide a comprehensive summary of the latest methodological advancements and emerging patterns in utilizing lipidomics in clinical research.In this review, we assess the recent advancements in lipidomics methodologies that exhibit high levels of selectivity and sensitivity, capable of generating numerous molecular lipid species from limited quantities of biological matrices. The reviewed studies demonstrate that molecular lipid signatures offer new opportunities for precision medicine by providing sensitive diagnostic tools for disease prediction and monitoring. Moreover, the latest innovations in microsampling techniques have the potential to make a substantial contribution to clinical lipidomics. The review also shows that more work is needed to harmonize results across diverse lipidomics platforms and avoid significant errors in analysis and reporting. The increased implementation of internal standards and standard reference materials in analytical workflows will aid in this direction.